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(-) Description

Title :  CRYSTAL STRUCTURE OF LGG-1 COMPLEXED WITH A WEEL PEPTIDE
 
Authors :  Y. Watanabe, N. N. Noda
Date :  05 Oct 15  (Deposition) - 30 Dec 15  (Release) - 30 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Autophagy, Ubiquitin-Like, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Wu, Y. Watanabe, X. Y. Guo, X. Qi, P. Wang, H. Y. Zhao, Z. Wang, Y. Fujioka, H. Zhang, J. Q. Ren, T. C. Fang, Y. X. Shen, W. Feng, J. J. Hu, N. N. Noda, H. Zhang
Structural Basis Of The Differential Function Of The Two C. Elegans Atg8 Homologs, Lgg-1 And Lgg-2, In Autophagy
Mol. Cell V. 60 914 2015
PubMed: search  |  Reference-DOI: 10.1016/J.MOLCEL.2015.11.019

(-) Compounds

Molecule 1 - PROTEIN LGG-1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX-6P
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-116
    Gene: LGG-1, C32D5.9
    Organism Scientific: CAENORHABDITIS ELEGANS
    Organism Taxid: 6239
 
Molecule 2 - PEPTIDE FROM AUTOPHAGY-RELATED PROTEIN 19
    Chains: C, D
    Engineered: YES
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: ATG19 AIM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1CD13Ligand/IonCADMIUM ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:42 , ASP A:97 , HOH A:347 , HOH A:426 , HOH A:428 , HOH A:435binding site for residue CD A 201
02AC2SOFTWAREHIS A:98 , HOH A:338 , HOH A:432 , HOH A:439 , HOH A:451 , HOH A:490binding site for residue CD A 202
03AC3SOFTWAREHIS A:99 , CD A:205 , HOH A:374 , HOH A:445 , HOH A:461 , HOH A:462binding site for residue CD A 203
04AC4SOFTWAREHIS A:0 , GLY A:116 , GLY B:-2 , HOH B:394 , HOH B:396binding site for residue CD A 204
05AC5SOFTWAREHIS A:99 , CD A:203 , HOH A:374 , HOH A:434binding site for residue CD A 205
06AC6SOFTWAREHIS B:42 , ASP B:97 , HOH B:346 , HOH B:429 , HOH B:441 , HOH B:445binding site for residue CD B 201
07AC7SOFTWAREHIS B:98 , HOH B:319 , HOH B:436 , HOH B:452 , HOH B:455 , HOH B:482binding site for residue CD B 202
08AC8SOFTWAREHIS B:99 , CD B:207 , HOH B:369 , HOH B:458 , HOH B:467binding site for residue CD B 203
09AC9SOFTWAREGLY A:-2 , HOH A:337 , HOH A:388 , HIS B:0 , GLY B:116binding site for residue CD B 204
10AD1SOFTWAREASP B:27 , HOH B:410 , HOH B:437 , TRP C:1 , HOH C:109binding site for residue CD B 205
11AD2SOFTWAREGLU B:17binding site for residue CD B 206
12AD3SOFTWAREHIS B:99 , CD B:203 , HOH B:369 , HOH B:412binding site for residue CD B 207
13AD4SOFTWARELYS B:46 , LYS B:47 , LYS B:48 , HOH B:311 , HOH B:326binding site for residue SO4 B 208
14AD5SOFTWARETRP D:1 , HOH D:201 , HOH D:205 , HOH D:209binding site for residue CD D 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AZF)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AZF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AZF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AZF)

(-) Exons   (0, 0)

(no "Exon" information available for 5AZF)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee............eeee....hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5azf A  -2 GPHMKWAYKEENNFEKRRAEGDKIRRKYPDRIPVIVEKAPKSKLHDLDKKKYLVPSDLTVGQFYFLIRKRIQLRPEDALFFFVNNVIPQTMTTMGQLYQDHHEEDLFLYIAYSDESVYG 116
                                     7        17        27        37        47        57        67        77        87        97       107         


Chain B from PDB  Type:PROTEIN  Length:119
                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhh..eeeeeeee............eeeee...hhhhhhhhhhhhh........eee..........hhhhhhhhhh.....eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 5azf B  -2 GPHMKWAYKEENNFEKRRAEGDKIRRKYPDRIPVIVEKAPKSKLHDLDKKKYLVPSDLTVGQFYFLIRKRIQLRPEDALFFFVNNVIPQTMTTMGQLYQDHHEEDLFLYIAYSDESVYG 116
                                     7        17        27        37        47        57        67        77        87        97       107         


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5azf C   1 WEEL   4


Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5azf D   1 WEEL   4
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5AZF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AZF)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AZF)

(-) Gene Ontology  (31, 35)

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  LGG1_CAEEL | Q09490
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ATG19_YEAST | P35193: 2kzb 2zpn 5jge
        LGG1_CAEEL | Q09490: 5azg

(-) Related Entries Specified in the PDB File

5azg 5azh